A2.3: Microbes in The News

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Article and Link:

Hello, Little Microbe. Doesn’t This Jacket Look Yummy?

Now we can trick tiny bugs into eating our clothing. Consumption is finally a good thing.

By Vanessa Friedman in The New York Times on April 22, 2019

Image Credit: Photo Illustration by Tracy Ma/The New York Times; Courtesy of PrimaLoft (jacket).

https://www.nytimes.com/2019/04/22/fashion/biodegradable-clothing-sustainability.html

Summary:

While this article was in the fashion section of The New York Times, it concerned the modification of clothing by attaching microbe-attracting sugars to polyester fibers used in clothing. This would allow the expedited degradation of fabrics by producing a new niche for microbes, both in landfill and marine environments.

Connections:

In lecture, we have discussed microbe niches, and microbial carbon sources.

Critical Analysis:

This was not a scientific article by any means, but did contain accurate information about microbial preference for less-synthetic carbon sources. While the authors report that the textile company it interviewed would not reveal “proprietary processes” for how polyester fibers would be modified, they did mention that testing of the modified fibers was being conducted over several years, and in both marine and landfill environments. For a non-science article, I thought it did a great job of identifying a problem (the massive amount of clothing taking decades to degrade), identifying a scientific solution (speeding up bio-degradation) and explaining just enough about the solution (microbes!) to make it approachable for the average fashion-section reader. I would have liked a link or reference, but like any science-minded person, I have enough to go on to look into it further. It was beyond the scope of this publication to consider concerns such as biofilms or the potential for increased infections from wearing microbe-attracting clothing. I’m sure these considerations will be investigated as these fibers move into the mainstream.

Question:

One field which has very close ties to microbiology is forensics. The microbial effects on evidence in various environments is a crucial aspect of these studies. How will a new generation of clothing with different bio-degradation rates affect this field?

References:

Ueland, M.  et al. (2017). Degradation patterns of natural and synthetic textiles on a soil surface during summer and winter seasons studied using ATR-FTIR spectroscopy. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 185. doi: 10.1016/j.saa.2017.05.044.

Third Microbes in the News

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— Article and link: A Blazing Hot Coal Shows How Microbes Can Spring to Life   Source: Wired 04/21/19   Link: https://www.wired.com/story/a-blazing-hot-coal-seam-shows-how-microbes-can-spring-to-life/

— Summary: In Centralia many single-celled microbes live in the soil that is on top of the underground mine fire in the coal seam. Due to the fire it was initially thought nothing may have lived, but instead there are many microbes. The same amount of microbes have been found to be living in very hot areas including various thermophiles that microbes that live at geothermal hot springs.

— Connections: In class we have briefly studied thermophiles which are heat loving bacteria. We have also looked at the various species of microbes that live in soil, and I find it interesting how natural disasters can affect what microbes are in the soil. We studied factors that can cause microbes to go dormant, which is what can happen during a fire since there is no activity on the soil.

— Critical analysis: I thought this article was interesting because it involves microbe activity when a natural disaster occurs and using spores to regrow genomes. The article was well written and contained a large amount of detailed scientific information. It could be rather difficult for the general public to read the article and understand it all though, because of all the technical terms it contains.

— Question: What organisms do you think would be likely to live through a fire or other extreme natural disaster? Would they become dormant?

 

 

Micro Magnets

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Art Project: Micro Magnets

by Emily Reast

For this project I’ve made a series of color coded clay magnets representing different   types of microbes. I want to show that microbial life can be interesting, presenting diversity, and that it can be beautiful (even if I’m not the best artist). The green magnets represent bacteria, the blue yeast (fungi), the orange and red viruses, and the purples archaea. I’ve included some features such as flagella and pili on several of the magnets to make them appear slightly more realistic. Of course the different microbes are not accurate in their relative size to each other, but I had limited resources and didn’t want to make any of the art actually be microscopic. Furthermore, the quality of being magnetic allows the microbes to change orientations and colony formation on the surface to which they stick. The photo attached to this post is the magnets stuck to my dorm room door here on campus.

A2: Microbes in the News (#2)

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How electricity-eating microbes use electrons to fix carbon dioxide (Science Daily)

Find the article  here.

Summary:   The bacterium, Rhodopseudomonas palustris, has been identified to have the ability to metabolize electricity. It transfers electrons to fix CO2 to fuel its growth. Essentially, it enjoys feasting on rust and uses the electrons in a process called extracellular electron uptake. The research team at Washington University are using this knowledge to understand the microbe’s role in carbon cycling and has helped connect some unknown areas of basic concepts.

An understanding of how these microbes store the electrons could potentially lead to the production of alternative biofuels.

Connection: The electron tower helped to visualize which compounds are metabolized by a microbe in question. We’ve also talked about the use of microbes in our everyday lives (probiotics, waste water treatment, immunizations, etc.), and could potentially lead to an alternative energy source if researchers discover the mechanisms to harness this microbe for bioplastics or biofuel (as mentioned in the article).

Critical Analysis: This could potentially lead to a great alternative source for fuels in the future.   It’s in its exploratory stages currently and much more about specific mechanisms needs to be learned before researchers are ready to turn it into biofuel.

The draw back of this type of approach poses the concern about how this application will alter the microbial world around us. Other fuels accumulate in the atmosphere so how will the accumulation of an organism affect our environment?

 

Question: How could the artificial abundance of this microbe affect the ecosystems around it?

 

 

 

Pumping May Alter the Microbes in Breast Milk

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Article: “Pumping may be linked to an altered microbial mix in breast milk” by Laura Sanders

https://www.sciencenews.org/blog/growth-curve/pumping-may-be-linked-altered-microbial-mix-breast-milk

Source:  Science News

Date Published:  April 1, 2019

Summary:  A study compared the microbial makeup of breast milk from mothers who do not pump at all to breast milk from mothers who pump.   Although the microbes in breast milk is fairly unique from person to person, the researchers found two main differences.   The milk from women who pumped had more bacteria that could cause infections under optimal conditions and fewer bifidobacteria, which are thought to be beneficial bacteria.   It is still unknown as to what impact these differences have on the children, if any, and the origin for these bacteria is also under debate.   Some believe the bacteria from the gut travel to the breast and get into the milk, while others think that babies’ oral bacteria affects the bacteria in the breast.   There is some evidence that ‘baby backwash’ might trigger infection-fighting proteins in milk when the baby is fed directly from the breast, so this would not occur in milk that is pumped.

Connections:  This is related to what we were talking about with the human microbiome and how it can be affected by many different factors.   The way a mother feeds her baby not only affects the microbiome of the baby but the microbiome of her breast and breast milk, as well.

Critical Analysis:  I did not know that the way a baby receives breast milk can change the type of bacteria that occur within the breast milk itself.   Since the milk is made within the mother, I thought that only factors within the mother would affect it, so it is really interesting that babies play such a large role in that microbiome.   The information appears to be scientifically accurate since the author included some quotes from one of the scientists who did the research and did not add much of her own opinion when talking about the information from the research.   It was written well to relay the information from the scientists to people who may not have any science background.   It was easy to understand and follow.

Question:  Once the mother is done breast feeding, do any of the microbes remain in the breast?   Do they get flushed out with the milk or die?   If they do remain, are they there for the rest of her life or will they eventually go away?

A6: Painting with Microbes

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Emily Werner

F02

Escherichia coli- I used this on the EMB agar because it ferments lactose with the specific differential media and creates a green sheen color to it. I thought this would be appropriate for the northern lights.

Enterobacter aerogenes- The color of this microbe is a yellow-white. I used it for the moon and the stars in the photo. The bacteria is anaerobic because it too turned black on the media due to fermentation. I had overlooked that when choosing the bacteria. The stars that I dabbed onto the plate didn’t show up so I’m thinking that there wasn’t enough bacteria present to start a colony or it was still undergoing the lag phase of replication.

Citrobacter freundii-   This was used for the river and the mountains. I wanted to go for a shadow style look for the mountains.

 

Each bacteria was gram negative so they showed up well on the plate as this agar specifically selects for only gram-negative. The agar was a dark red to begin with but lightened up over the course of 4 days.

 

 

New technique provides a better understanding of bacteria evolution

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New technique pinpoints milestones in the evolution of bacteria
Results show bacterial genomes provide “shadow history’ of animal evolution.
Jennifer Chu, MIT News Office February 7, 2019

References

Danielle S. Gruen, J. M. (2019, January). Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19-34. Retrieved from https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1357-8

 

—  Summary:  Researchers from MIT have established organism relationships between fungi and bacteria by reviewing the gene for chitinase (an enzyme which helps to break down chitin). Their review of the mutations, and similarities across different species has allowed them to create an evolutionary tree which correlates microbial evolution with fungal evolution. They found that approximately 450 to 350 million years ago, diversification of three separate bacterial groups diversified as the result of gene transfer with a chitinase utilizing fungi. Below is the resulting evolutionary tree with the fungi identified by purple lines and bacteria with blue lines.

(Gruen, et al. 2019)

—  Connections:  This connects with: Microbial evolution, metabolism, and diversification.
Chitinase allows these bacteria to metabolize chitin as an energy source. This allowed diversification of microbes into new niches ones chitin became more prolific in the environment. Gene transfer was said to make it difficult to genomically identify or differentiate bacterial strains, but here the gene transfer has allowed a better understanding.

—  Critical analysis: I found this article very interesting because, most evolutionary trees are based on rRNA sequencing (highly conserved due to form/function). The use of chitinase to correlate evolutionary relationships between fungus and bacteria is interesting. Especially since the origin of chitinase was in a Fungi (a microorganism that doesn’t look like a microorganism) and the gene has been horizontally transferred to bacteria.

The story was very well written and after reading the original journal publication, it was factually and accurately written. The author did as great job in conveying the information to the general population without losing the integrity of the research. I appreciate the writing style and how it helps those (like myself) who aren’t as well versed in the scientific nomenclature, to understand the information and findings from the research.

 

—  Question:  How many other highly conserved coding regions can we isolate and use in this manner? Are enzymes such as chitinase always highly conserved, or is there slight variations in the conformation, allowing it to mutate without ruining the function of the enzyme?

-Samantha Smith

A Rising Threat to Pregnant Women: Syphilis

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Title: A Rising Threat to Pregnant Women: Syphilis

 

Summary: Syphilis, which is a sexually transmitted bacterial infection, has been increasing in women (including pregnant women) all over the United States in recent years. This is especially dangerous, because babies that are born with syphilis have a 40% chance of being born stillborn. All pregnant women should be tested for syphilis multiple times during pregnancy, because they can contract it after they are already pregnant. If someone is tested positive, penicillin will be prescribed, and it has a 98% effectiveness rate.

 

Connections: In the first week of class we talked about the history of discovering microbes, and while this isn’t a discovery, it is important to utilize tests and treatments that were previously discovered so that diseases don’t continue to be spread.

 

Critical Analysis: While I knew STDs could be passed from mother to child, I hadn’t really thought about how dangerous it could be until I read this article. However, this was a very brief article, so I kind of wish it could have gone into more details about syphilis and how it spread in order to inform the public. I couldn’t find anything intentionally misleading, but its possible some of the statistics were. The only thing that I thought was kind of strange was how they framed the article specifically around pregnant women, and then explained how syphilis has actually just been increasing in women in general. I think this was a short and to the point article that helped inform people that syphilis is dangerous, especially during pregnancy, and that it is importance to get testing and treatment.

 

Question: This article frames the recent rise in syphilis specifically around pregnant women, even though it is increasing in all women. Was this the article trying to be more sensational, in order to reach more people, and is this a helpful tactic to inform people about dangerous infections? What is the best way to inform people about a bacterial infection that doesn’t initially have obvious symptoms?

A3: Epithet Epitaphs

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Caloustegulbenkian.jpg

Microbial Species:

Gulbenkiania mobilis

Genus Namesake:

Calouste Gulbenkian

Latin Binomial:

mobilis; movable or motile

Brief Biography:

Calouste Gulbenkian was born March 23, 1869 in what is now Istanbul, Turkey. His father was deeply involved in oil import/export. After Calouste’s education in Armenian and French schools, he studied at Robert College in Istanbul and King’s College in London, earning a degree in petroleum engineering. Following his father’s footsteps, he started his own oil operations business in 1895. The next year he fled the Armenian Massacres and formed a network of wealthy and influential contacts in Egypt. He then moved to London and conducted business deals with the aid of his contacts. He arranged mergers and developed multiple oil companies, most notably the Iraq Petroleum Company. His role in the development of that company and others resulted in his nickname, “Mr. Five Percent.” The retention of five percent of the shares of companies he handled fueled his massive acquisition of wealth. As a billionaire, he owned several homes and amassed a huge art collection. He also donated millions of dollars, mainly to Armenian establishments. He was a benefactor to churches, hospitals, a library, and to settlements for refugees from the Armenian Genocide. Gulbenkian spent the last thirteen years of his life in Lisbon, Portugal, and willed a large portion of his fortune to the establishment of the Calouste Gulbenkian Foundation there. The Foundation promotes arts, charity, education, and science throughout the world. Much of Calouste’s art is housed at the Calouste Gulbenkian Museum in Lisbon. At his death in 1955 he was reportedly the world’s richest man.

References:

Calouste Gulbenkian. (2019). In Wikipedia. Retrieved January 27, 2019, from  https://en.wikipedia.org/wiki/Calouste_Gulbenkian.

Calouste Gulbenkian Foundation. (2019). Last Years in Lisbon. Retrieved January 27, 2019 from https://gulbenkian.pt/en/the-foundation/calouste-sarkis-gulbenkian/last-years-in-lisbon/.

Conlin, J. (2019) Mr. Five Per Cent: The Many Lives of Calouste Gulbenkian, the World’s Richest Man. [Kindle Editions version]. Retrieved from https://www.amazon.com.

A2: Microbes in the News

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Article and Link:

Microbes Might Be Key to a Mars Mission

Engineered yeast could turn waste into food, plastics and other essentials

By Mark Blenner on January 14, 2019

Microbes Might Be Key to a Mars Mission

Image Credit: NASA, Clouds AO and SEArch Wikimedia

Blenner, M. (2019, January). Microbes Might be Key to a Mars Mission.  Scientific American.  Retrieved from  https://blogs.scientificamerican.com/

Summary:

The author describes the work of his team as they engineer modified versions of the yeast  Yarrowia liplytica.  Dr. Blenner suggests strains of the modified yeast could survive on waste products from astronauts while creating materials to facilitate repairs and improve astronaut health. Genes “borrowed” from other organisms could allow the modified yeast to generate useful products. For example, these products could be used as the building blocks for 3-D printed parts or for adhesives used for repairs. One strain of the modified yeast uses genes “cut and pasted” from plants and algae to produce eicosapentaenoic acid (EPA). This valuable Omega-3 fatty acid is a neutraceutical known to help prevent bone density loss in astronauts.

Connections:

In lecture, we discussed yeast as a model species. This organism is often mistaken for a prokaryote by new biology students, perhaps because it is small and single-celled. These fungi have a membrane-bound nucleus, however, and are thus eukaryotes. Use of yeast strains as model species predates work begun by Dr. Blenner in 2012.

In lecture we also touched on synthetic biology, and its similarity to traditional genetic engineering. In genetic engineering, genes known to code for products resulting in desired traits are “added to” an organism’s genome. The desired traits referred to in this article are: 1) the consumption of astronaut waste products and 2) the production of products useful to astronauts during space travel.

Finally, a Microbes in the News article posted by @kcallegari discusses the hardy nature of microbes found in the International Space Station (ISS). I think the evidence of mutations in the bacteria found in the ISS may have applications in the engineering of the yeast strains Dr. Blenner’s team is working with. I think it would be interesting to consider what mutations are already present in the “space generations” of bacteria, and what might happen if similar mutations occur in modified fungi.

Critical Analysis:

This blog was written in a conversational, non-jargon language which made the main points easy for anyone to understand.   Dr. Blenner referenced a recent scientific publication, and gave a one-sentence summary of those findings (Brabender 2018). He then connected this to his current research, which validated the need for this avenue of investigation. This was effective scientific communication because raising awareness of potential benefits to this area of study is the best way to bolster interest and thus funding for further research.

I felt there was some implication that the products from the modified yeast strains were sure to be useful to astronauts, which isn’t supported by the findings he presented in this article. However, I can understand that determining how to harvest and utilize those products and proving that the processes would be worth the time and tools it might take wasn’t the purview of the current study. This may be the next stage of study for his team, or may be the task for another team of scientists. Perhaps acknowledging the limitations of the current study may have made the need for future supporting studies seem less glossed-over.

I thought citing his background in studies of synthetic biology and yeast helped to authenticate Dr. Blenner’s article, as did his bio, which notes the funding source for the current research. In all; the article identified a real-world need, referenced published scientific literature, explained how the current study aimed to address the real-world need, and suggested potential benefits of further study. It was an effective use of the blog forum to garner awareness and potential support both for his team’s current research and for future studies.

Question:

I understand scientists use model species because these species have characteristics universal enough to apply to other species across the tree of life. In the studies this article describes, the DNA regions of interest being transferred are from simple organism to simple organism. The regions cut and pasted into other organisms’ genomes can include one gene or several genes, as well as parts of the non-coding regions surrounding those genes. This may have relatively straightforward results in single celled organisms. Yet in multi-celled organisms, there are innumerable inter-systemic interactions in the micro-chemistry unique to each species. For example, a single neurotransmitter can affect both brain chemistry and gut processes (Li 2004). Is it productive and ethical to experiment with inserting regions of interest into more complex species before the biochemistry of inter-dependent bio-systems are fully mapped out?

References:

Brabender, M., Hussain, M.S., Rodriguez, G. et al. Urea and urine are a viable and cost-effective nitrogen source for  Yarrowia lipolytica  biomass and lipid accumulation. Applied Microbiol Biotechnology (2018) 102: 2313. doi.org/10.1007/s00253-018-8769-z.

Li, Z.S.,  T. D. Pham,  H. Tamir,  J. J. Chen  and  M. D. Gershon.  Enteric Dopaminergic Neurons: Definition, Developmental Lineage, and Effects of Extrinsic Denervation.  Journal of Neuroscience  (2004)  24:  1330-1339.  doi.org/10.1523/JNEUROSCI.3982-03.2004.